Link page A to page E and click Calculate. Notice that the site’s total has gone down very significantly. But, because the new link is dangling and would be removed from the calculations, we can ignore the new total and assume the previous 4.15 to be true. That’s the effect of functionally useful, dangling links in the site. There’s no overall PageRank loss.
Another excellent guide is Google’s “Search Engine Optimization Starter Guide.” This is a free PDF download that covers basic tips that Google provides to its own employees on how to get listed. You’ll find it here. Also well worth checking out is Moz’s “Beginner’s Guide To SEO,” which you’ll find here, and the SEO Success Pyramid from Small Business Search Marketing.